static void singlequerymatchspacedseed(Limdfsresources *limdfsresources,
const AbstractDfstransformer *dfst,
const GtUchar *query,
GtUword querylen,
const Spacedseed *spse)
{
const GtUchar *qptr;
GtUword offset, skipvalue;
if (spse->seedwidth > querylen)
{
return;
}
qptr = query;
offset = 0;
while (qptr <= query + querylen - spse->seedwidth)
{
skipvalue = containsspecialbytestring(qptr,offset,spse->seedwidth);
if (skipvalue == spse->seedwidth)
{
offset = spse->seedwidth-1;
singlewindowmatchspacedseed(limdfsresources,dfst,qptr,spse);
qptr++;
} else
{
offset = 0;
qptr += (skipvalue+1);
}
}
}
static void singleseqtyrsearch(const Tyrindex *tyrindex,
const Tyrcountinfo *tyrcountinfo,
const Tyrsearchinfo *tyrsearchinfo,
const Tyrbckinfo *tyrbckinfo,
uint64_t unitnum,
const GtUchar *query,
unsigned long querylen,
GT_UNUSED const char *desc)
{
const GtUchar *qptr, *result;
unsigned long offset, skipvalue;
if (tyrsearchinfo->mersize > querylen)
{
return;
}
qptr = query;
offset = 0;
while (qptr <= query + querylen - tyrsearchinfo->mersize)
{
skipvalue = containsspecialbytestring(qptr,offset,tyrsearchinfo->mersize);
if (skipvalue == tyrsearchinfo->mersize)
{
offset = tyrsearchinfo->mersize-1;
if (tyrsearchinfo->searchstrand & STRAND_FORWARD)
{
result = gt_searchsinglemer(qptr,tyrindex,tyrsearchinfo,tyrbckinfo);
if (result != NULL)
{
mermatchoutput(tyrindex,
tyrcountinfo,
tyrsearchinfo,
result,
query,
qptr,
unitnum,
true);
}
}
if (tyrsearchinfo->searchstrand & STRAND_REVERSE)
{
gt_assert(tyrsearchinfo->rcbuf != NULL);
gt_copy_reversecomplement(tyrsearchinfo->rcbuf,qptr,
tyrsearchinfo->mersize);
result = gt_searchsinglemer(tyrsearchinfo->rcbuf,tyrindex,
tyrsearchinfo,tyrbckinfo);
if (result != NULL)
{
mermatchoutput(tyrindex,
tyrcountinfo,
tyrsearchinfo,
result,
query,
qptr,
unitnum,
false);
}
}
qptr++;
} else
{
offset = 0;
qptr += (skipvalue+1);
}
}
}